Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea

Abstract

Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.

Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.)

“…Molecular markers have been routinely used in breeding programs for trait dissection and mapping, evaluating genetic diversity, estimating evolutionary relationships, and marker‐assisted selection strategies (Roorkiwal et al., 2020). In general, QTL mapping (Roorkiwal et al., 2018; Sivashakthi et al., 2018; Soren et al., 2020) and association mapping (Varshney et al., 2012b, 2019) are used for identification of molecular marker(s) associated with the trait of interest. In the current study, we used a QTL mapping approach for an interspecific RIL population (ICC 4958 × PI 489777) for understanding the genetic architecture of H. armigera resistance component traits.…”

Application of Genomics to Understand Salt Tolerance in Lentil

“…Based on previous studies, most of these transporter genes, kinases, and transcription factors are reported to play an essential role in a salt stress response [1,10,75,76]. However, the importance of them in the salt tolerance mechanism in lentil is not known.…”

“…Soil salinity is identified as the second most significant abiotic stress after drought and in lentil (Lens culinaris Medik. ), salt toxicity typically causes between 20% and 100% reduction in plant growth and seed yield [1,2]. In Australia, c. 32 million ha of agricultural land is recognized as highly saline [3,4], therefore, lentil cultivation is limited to an area of c. 360,120 ha with an annual production of 533,755 tonnes, thus making Australia the third largest producer of lentil in the world [5].…”

“…Therefore, an alternative approach is to understand the genetic basis of salt responsive traits and develop salt-tolerant cultivars. Many other grain legumes and higher plants have attempted this approach for abiotic and biotic characteristics, including soil salinity [1,20,21]. Recently, GWAS has been used as a powerful tool to dissect the genetic basis of many phenotypic traits using genetically diverse populations [22,23].…”

“…However, rapid improvements in low-cost next-generation sequencing (NGS) and advances in accurate resequencing based on novel genotyping-by-sequencing (GBS) have enabled the GWAS in many grain crops [1,21,28]. Currently, numerous GBS methods are available, broadly classified into genome complexity reduction-based methods (e.g., restriction enzyme-based, transcriptome-based) and target enrichment/target capture (e.g., PCR amplification, molecular inversion probes (MIPS) and hybrid capture) [30].…”